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Rare Event Detection Using Error-corrected DNA and RNA Sequencing
Published on: August 3, 2018
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Palindromic sequence artifacts generated during next generation sequencing library preparation from historic and
Bastiaan Star1, Alexander J Nederbragt1, Marianne H S Hansen1
1Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.
Plos One
|March 11, 2014
Summary
A novel DNA sequencing artifact, forming interrupted palindromes, has been identified in historic Atlantic cod samples. This artifact, caused by hairpin loops in single-stranded DNA, introduces sequence bias and affects DNA yield in ancient DNA studies.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Ancient and historic DNA samples are susceptible to degradation and laboratory biases.
- Sequence composition can be skewed by DNA damage and specific library preparation methods.
Purpose of the Study:
- To identify and characterize novel artifacts in DNA sequences from historic samples.
- To understand the mechanisms behind sequence bias in ancient DNA (aDNA) studies.
Main Methods:
- Analysis of DNA sequences from historic Atlantic cod (Gadus morhua) samples.
- Identification of sequence patterns, including interrupted palindromes.
- Comparison with existing ancient DNA datasets.
Main Results:
- A novel artifact characterized by interrupted palindromes at the 5' and 3' ends of sequencing reads was identified.
- These palindromes result from hairpin loop formation in single-stranded DNA (ssDNA).
- The artifact was observed in historic samples and at lower frequencies in published aDNA datasets, causing sequence bias and reduced endogenous DNA yield.
Conclusions:
- The identified artifact significantly impacts the accuracy of DNA sequencing from historic and ancient samples.
- Understanding this artifact is crucial for improving library preparation protocols and data analysis in paleogenomics.
- This finding highlights the need for careful quality control in ancient DNA research.
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